Related papers: Watching Single Unmodified Enzymes at Work
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
We report on an experimental investigation of the dynamics of entanglement between a single qubit and its environment, as well as for pairs of qubits interacting independently with individual environments, using photons obtained from…
Synapses change on multiple timescales, ranging from milliseconds to minutes, due to a combination of both short- and long-term plasticity. Here we develop an extension of the common Generalized Linear Model to infer both short- and…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
Direct real time studies of reacting individual atoms in technologically important gold and platinum nanocatalysts in controlled reducing and oxidising gas environments and operating temperatures using novel environmental scanning…
The dynamics of peptide-protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its…
Kinesins are processive motor proteins that move along microtubules in a stepwise manner, and their motion is powered by the hydrolysis of ATP. Recent experiments have investigated the coupling between the individual steps of single kinesin…
The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse (IS). Understanding the biophysical basis for protein patterning by deciphering the…
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics…
We present a detailed dynamic light scattering study on the phase separation in the ocular lens emerging during cold cataract development. Cold cataract is a phase separation effect that proceeds via spinodal decomposition of the lens…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…